Mercurial > repos > diodupima > phage_coast_search

diff phage_coast_search.xml @ 1:6a33bad2db7f draft default tip

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"planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702-dirty"
author diodupima
date Wed, 17 Nov 2021 11:11:00 +0000
parents fb0ce7937a85
children
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--- a/phage_coast_search.xml	Thu Jul 15 16:51:26 2021 +0000
+++ b/phage_coast_search.xml	Wed Nov 17 11:11:00 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="phage_coast_search" name="PhageCOAST - Search" version="0.1.2">
+<tool id="phage_coast_search" name="PhageCOAST - Search" version="0.2.0">
     <description>Run a new job, and identify the closest proteomes</description>
     <macros>
         <import>macros.xml</import>
@@ -7,20 +7,23 @@
         <expand macro="requirements"/>
     </requirements>
     <command><![CDATA[
-        coast
+        coast search
+        "$db"
         @QUERY@
-        "$db"
         --engine blast
         --inplace_workspace
-        @AAI_FILTER@
-        @OUTPUT@
         @QUERY_KEYWORDS@
-        @OUTPUT_FORMAT@
         @BLAST_TAX_FILTER@
         @BLAST_ALN_OPTIONS@
         @GENERIC_ALN_OPTIONS@
-        -w 'http://rosalind.di.uminho.pt:6082/'
+        --web 'http://rosalind.di.uminho.pt:6082/'
         --email phage@coast.um
+        && coast report
+        "blast_results.tab"
+        @QUERY@
+        @AAI_FILTER@
+        @OUTPUT_FORMAT@
+        @QUERY_KEYWORDS@
     ]]></command>
     <inputs>
         <expand macro="input_query" />